EHV-1 TSS dynamics
Balázs Kakuk
## Error in library(future.apply) :
## there is no package called 'future.apply'Project info
Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)
Canonic TSS dynamics
Those reads were counted only, where the 5-prime adapters were “correct” (according to LoRTIA)
Statistics of counts
Difference from mean
Varcoeff
Clustering of samples
## Bootstrap (r = 0.49)... Done.## Bootstrap (r = 0.59)... Done.## Bootstrap (r = 0.7)... Done.## Bootstrap (r = 0.8)... Done.## Bootstrap (r = 0.9)... Done.## Bootstrap (r = 1.0)... Done.## Bootstrap (r = 1.09)... Done.## Bootstrap (r = 1.19)... Done.## Bootstrap (r = 1.29)... Done.## Bootstrap (r = 1.39)... Done.
The sample 48h_3 stands out!
Filtering of samples
Clustering of genes into de-novo clusters using hierarchial clustering
Cluster memberships
## Bootstrap (r = 0.48)... Done.## Bootstrap (r = 0.59)... Done.## Bootstrap (r = 0.67)... Done.## Bootstrap (r = 0.78)... Done.## Bootstrap (r = 0.89)... Done.## Bootstrap (r = 1.0)... Done.## Bootstrap (r = 1.07)... Done.## Bootstrap (r = 1.19)... Done.## Bootstrap (r = 1.3)... Done.## Bootstrap (r = 1.37)... Done.Optimal number of clusters
Find the optimal number of clusters to cut the tree at and calculate
Clustering statistics: Cluster number: 5
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 2: 1 ORF4 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 3: 1 ORF5 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 4: 1 ORF7 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 5: 1 ORF9 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 6: 1 ORF10 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 7: 1 ORF17 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 8: 1 ORF20 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 9: 1 ORF21 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 10: 1 ORF30 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 11: 1 ORF31 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 12: 1 ORF32 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 13: 1 ORF34 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 14: 1 ORF38 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 15: 1 ORF50 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 16: 1 ORF53 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 17: 1 ORF56 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 18: 1 ORF61 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 19: 1 ORF63 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 20: 1 NOIR_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 21: 1 ORF65_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 22: 1 ORF67_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 23: 1 ORF69 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 24: 1 NOIR_2 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 25: 2 ORF2 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 26: 2 ORF3 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 27: 2 ORF11 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 28: 2 ORF14 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 29: 2 ORF18 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 30: 2 ORF19 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 31: 2 ORF26 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 32: 2 ORF28 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 33: 2 ORF29 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 34: 2 ORF37 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 35: 2 ORF49 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 36: 2 ORF51 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 37: 2 ORF55 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 38: 2 ORF66_1 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 39: 2 ORF73 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 40: 2 ORF74 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 41: 2 ORF76 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 42: 3 ORF6 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 43: 3 ORF70 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 44: 4 ORF8 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 45: 4 ORF12 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 46: 4 ORF13 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 47: 4 ORF15 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 48: 4 ORF16 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 49: 4 ORF22 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 50: 4 ORF23 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 51: 4 ORF24 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 52: 4 ORF25 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 53: 4 ORF27 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 54: 4 ORF33 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 55: 4 ORF35.5 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 56: 4 ORF35 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 57: 4 ORF36 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 58: 4 ORF39 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 59: 4 CTO 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 60: 4 ORF40 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 61: 4 ORF41 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 62: 4 ORF42 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 63: 4 ORF43 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 64: 4 ORF44 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 65: 4 ORF45 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 66: 4 ORF46 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 67: 4 ORF48 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 68: 4 ORF52 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 69: 4 ORF54 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 70: 4 ORF57 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 71: 4 ORF58 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 72: 4 ORF59 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 73: 4 ORF60 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 74: 4 ORF62 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 75: 4 ORF68 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 76: 4 ORF71 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 77: 4 ORF72 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 78: 5 ORF64_1 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 79: 5 ORF75 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004412661 -1.9247386 1.0297672 0.6455362
## 2: 0.004412661 -1.9247386 1.0297672 0.6455362
## 3: 0.004412661 -1.9247386 1.0297672 0.6455362
## 4: 0.004412661 -1.9247386 1.0297672 0.6455362
## 5: 0.004412661 -1.9247386 1.0297672 0.6455362
## 6: 0.004412661 -1.9247386 1.0297672 0.6455362
## 7: 0.004412661 -1.9247386 1.0297672 0.6455362
## 8: 0.004412661 -1.9247386 1.0297672 0.6455362
## 9: 0.004412661 -1.9247386 1.0297672 0.6455362
## 10: 0.004412661 -1.9247386 1.0297672 0.6455362
## 11: 0.004412661 -1.9247386 1.0297672 0.6455362
## 12: 0.004412661 -1.9247386 1.0297672 0.6455362
## 13: 0.004412661 -1.9247386 1.0297672 0.6455362
## 14: 0.004412661 -1.9247386 1.0297672 0.6455362
## 15: 0.004412661 -1.9247386 1.0297672 0.6455362
## 16: 0.004412661 -1.9247386 1.0297672 0.6455362
## 17: 0.004412661 -1.9247386 1.0297672 0.6455362
## 18: 0.004412661 -1.9247386 1.0297672 0.6455362
## 19: 0.004412661 -1.9247386 1.0297672 0.6455362
## 20: 0.004412661 -1.9247386 1.0297672 0.6455362
## 21: 0.004412661 -1.9247386 1.0297672 0.6455362
## 22: 0.004412661 -1.9247386 1.0297672 0.6455362
## 23: 0.004412661 -1.9247386 1.0297672 0.6455362
## 24: 0.004412661 -1.9247386 1.0297672 0.6455362
## 25: 0.005151525 -0.8707344 0.5400240 0.2113619
## 26: 0.005151525 -0.8707344 0.5400240 0.2113619
## 27: 0.005151525 -0.8707344 0.5400240 0.2113619
## 28: 0.005151525 -0.8707344 0.5400240 0.2113619
## 29: 0.005151525 -0.8707344 0.5400240 0.2113619
## 30: 0.005151525 -0.8707344 0.5400240 0.2113619
## 31: 0.005151525 -0.8707344 0.5400240 0.2113619
## 32: 0.005151525 -0.8707344 0.5400240 0.2113619
## 33: 0.005151525 -0.8707344 0.5400240 0.2113619
## 34: 0.005151525 -0.8707344 0.5400240 0.2113619
## 35: 0.005151525 -0.8707344 0.5400240 0.2113619
## 36: 0.005151525 -0.8707344 0.5400240 0.2113619
## 37: 0.005151525 -0.8707344 0.5400240 0.2113619
## 38: 0.005151525 -0.8707344 0.5400240 0.2113619
## 39: 0.005151525 -0.8707344 0.5400240 0.2113619
## 40: 0.005151525 -0.8707344 0.5400240 0.2113619
## 41: 0.005151525 -0.8707344 0.5400240 0.2113619
## 42: 0.004425869 -1.9892346 1.0926661 0.5323203
## 43: 0.004425869 -1.9892346 1.0926661 0.5323203
## 44: 0.005261677 -1.1191772 0.8688403 0.4684034
## 45: 0.005261677 -1.1191772 0.8688403 0.4684034
## 46: 0.005261677 -1.1191772 0.8688403 0.4684034
## 47: 0.005261677 -1.1191772 0.8688403 0.4684034
## 48: 0.005261677 -1.1191772 0.8688403 0.4684034
## 49: 0.005261677 -1.1191772 0.8688403 0.4684034
## 50: 0.005261677 -1.1191772 0.8688403 0.4684034
## 51: 0.005261677 -1.1191772 0.8688403 0.4684034
## 52: 0.005261677 -1.1191772 0.8688403 0.4684034
## 53: 0.005261677 -1.1191772 0.8688403 0.4684034
## 54: 0.005261677 -1.1191772 0.8688403 0.4684034
## 55: 0.005261677 -1.1191772 0.8688403 0.4684034
## 56: 0.005261677 -1.1191772 0.8688403 0.4684034
## 57: 0.005261677 -1.1191772 0.8688403 0.4684034
## 58: 0.005261677 -1.1191772 0.8688403 0.4684034
## 59: 0.005261677 -1.1191772 0.8688403 0.4684034
## 60: 0.005261677 -1.1191772 0.8688403 0.4684034
## 61: 0.005261677 -1.1191772 0.8688403 0.4684034
## 62: 0.005261677 -1.1191772 0.8688403 0.4684034
## 63: 0.005261677 -1.1191772 0.8688403 0.4684034
## 64: 0.005261677 -1.1191772 0.8688403 0.4684034
## 65: 0.005261677 -1.1191772 0.8688403 0.4684034
## 66: 0.005261677 -1.1191772 0.8688403 0.4684034
## 67: 0.005261677 -1.1191772 0.8688403 0.4684034
## 68: 0.005261677 -1.1191772 0.8688403 0.4684034
## 69: 0.005261677 -1.1191772 0.8688403 0.4684034
## 70: 0.005261677 -1.1191772 0.8688403 0.4684034
## 71: 0.005261677 -1.1191772 0.8688403 0.4684034
## 72: 0.005261677 -1.1191772 0.8688403 0.4684034
## 73: 0.005261677 -1.1191772 0.8688403 0.4684034
## 74: 0.005261677 -1.1191772 0.8688403 0.4684034
## 75: 0.005261677 -1.1191772 0.8688403 0.4684034
## 76: 0.005261677 -1.1191772 0.8688403 0.4684034
## 77: 0.005261677 -1.1191772 0.8688403 0.4684034
## 78: 0.005245917 -0.8139770 1.0031408 0.7004716
## 79: 0.005245917 -0.8139770 1.0031408 0.7004716
## se.bp v c pchi
## [1] "ORF32" "ORF9" "ORF67_1" "ORF40" "ORF59" "ORF36" "ORF39"
## [8] "ORF8"## [1] 8## [1] "ORF2" "ORF3" "ORF11" "ORF14" "ORF18" "ORF19" "ORF26"
## [8] "ORF28" "ORF29" "ORF37" "ORF49" "ORF51" "ORF55" "ORF66_1"
## [15] "ORF73" "ORF74" "ORF76"## [1] 17Clustering statistics: Cluster number: 6
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 2: 1 ORF4 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 3: 1 ORF5 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 4: 1 ORF7 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 5: 1 ORF9 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 6: 1 ORF10 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 7: 1 ORF17 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 8: 1 ORF20 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 9: 1 ORF21 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 10: 1 ORF30 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 11: 1 ORF31 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 12: 1 ORF32 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 13: 1 ORF34 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 14: 1 ORF38 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 15: 1 ORF50 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 16: 1 ORF53 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 17: 1 ORF56 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 18: 1 ORF61 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 19: 1 ORF63 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 20: 1 NOIR_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 21: 1 ORF65_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 22: 1 ORF67_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 23: 1 ORF69 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 24: 1 NOIR_2 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 25: 2 ORF2 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 26: 2 ORF3 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 27: 2 ORF11 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 28: 2 ORF14 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 29: 2 ORF18 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 30: 2 ORF19 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 31: 2 ORF26 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 32: 2 ORF28 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 33: 2 ORF29 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 34: 2 ORF37 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 35: 2 ORF49 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 36: 2 ORF51 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 37: 2 ORF55 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 38: 2 ORF66_1 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 39: 2 ORF73 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 40: 2 ORF74 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 41: 2 ORF76 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 42: 3 ORF6 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 43: 3 ORF70 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 44: 4 ORF8 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 45: 4 ORF12 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 46: 4 ORF13 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 47: 4 ORF15 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 48: 4 ORF16 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 49: 4 ORF22 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 50: 4 ORF23 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 51: 4 ORF24 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 52: 4 ORF25 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 53: 4 ORF27 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 54: 4 ORF33 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 55: 4 ORF35.5 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 56: 4 ORF35 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 57: 4 ORF36 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 58: 4 ORF39 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 59: 4 CTO 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 60: 4 ORF40 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 61: 4 ORF41 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 62: 4 ORF42 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 63: 4 ORF43 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 64: 4 ORF44 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 65: 4 ORF46 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 66: 4 ORF48 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 67: 4 ORF52 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 68: 4 ORF54 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 69: 4 ORF57 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 70: 4 ORF58 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 71: 4 ORF59 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 72: 4 ORF60 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 73: 4 ORF62 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 74: 4 ORF68 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 75: 4 ORF71 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 76: 4 ORF72 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 77: 5 ORF45 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 78: 6 ORF64_1 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 79: 6 ORF75 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004412661 -1.9247386 1.0297672 0.6455362
## 2: 0.004412661 -1.9247386 1.0297672 0.6455362
## 3: 0.004412661 -1.9247386 1.0297672 0.6455362
## 4: 0.004412661 -1.9247386 1.0297672 0.6455362
## 5: 0.004412661 -1.9247386 1.0297672 0.6455362
## 6: 0.004412661 -1.9247386 1.0297672 0.6455362
## 7: 0.004412661 -1.9247386 1.0297672 0.6455362
## 8: 0.004412661 -1.9247386 1.0297672 0.6455362
## 9: 0.004412661 -1.9247386 1.0297672 0.6455362
## 10: 0.004412661 -1.9247386 1.0297672 0.6455362
## 11: 0.004412661 -1.9247386 1.0297672 0.6455362
## 12: 0.004412661 -1.9247386 1.0297672 0.6455362
## 13: 0.004412661 -1.9247386 1.0297672 0.6455362
## 14: 0.004412661 -1.9247386 1.0297672 0.6455362
## 15: 0.004412661 -1.9247386 1.0297672 0.6455362
## 16: 0.004412661 -1.9247386 1.0297672 0.6455362
## 17: 0.004412661 -1.9247386 1.0297672 0.6455362
## 18: 0.004412661 -1.9247386 1.0297672 0.6455362
## 19: 0.004412661 -1.9247386 1.0297672 0.6455362
## 20: 0.004412661 -1.9247386 1.0297672 0.6455362
## 21: 0.004412661 -1.9247386 1.0297672 0.6455362
## 22: 0.004412661 -1.9247386 1.0297672 0.6455362
## 23: 0.004412661 -1.9247386 1.0297672 0.6455362
## 24: 0.004412661 -1.9247386 1.0297672 0.6455362
## 25: 0.005151525 -0.8707344 0.5400240 0.2113619
## 26: 0.005151525 -0.8707344 0.5400240 0.2113619
## 27: 0.005151525 -0.8707344 0.5400240 0.2113619
## 28: 0.005151525 -0.8707344 0.5400240 0.2113619
## 29: 0.005151525 -0.8707344 0.5400240 0.2113619
## 30: 0.005151525 -0.8707344 0.5400240 0.2113619
## 31: 0.005151525 -0.8707344 0.5400240 0.2113619
## 32: 0.005151525 -0.8707344 0.5400240 0.2113619
## 33: 0.005151525 -0.8707344 0.5400240 0.2113619
## 34: 0.005151525 -0.8707344 0.5400240 0.2113619
## 35: 0.005151525 -0.8707344 0.5400240 0.2113619
## 36: 0.005151525 -0.8707344 0.5400240 0.2113619
## 37: 0.005151525 -0.8707344 0.5400240 0.2113619
## 38: 0.005151525 -0.8707344 0.5400240 0.2113619
## 39: 0.005151525 -0.8707344 0.5400240 0.2113619
## 40: 0.005151525 -0.8707344 0.5400240 0.2113619
## 41: 0.005151525 -0.8707344 0.5400240 0.2113619
## 42: 0.004425869 -1.9892346 1.0926661 0.5323203
## 43: 0.004425869 -1.9892346 1.0926661 0.5323203
## 44: 0.005261677 -1.1191772 0.8688403 0.4684034
## 45: 0.005261677 -1.1191772 0.8688403 0.4684034
## 46: 0.005261677 -1.1191772 0.8688403 0.4684034
## 47: 0.005261677 -1.1191772 0.8688403 0.4684034
## 48: 0.005261677 -1.1191772 0.8688403 0.4684034
## 49: 0.005261677 -1.1191772 0.8688403 0.4684034
## 50: 0.005261677 -1.1191772 0.8688403 0.4684034
## 51: 0.005261677 -1.1191772 0.8688403 0.4684034
## 52: 0.005261677 -1.1191772 0.8688403 0.4684034
## 53: 0.005261677 -1.1191772 0.8688403 0.4684034
## 54: 0.005261677 -1.1191772 0.8688403 0.4684034
## 55: 0.005261677 -1.1191772 0.8688403 0.4684034
## 56: 0.005261677 -1.1191772 0.8688403 0.4684034
## 57: 0.005261677 -1.1191772 0.8688403 0.4684034
## 58: 0.005261677 -1.1191772 0.8688403 0.4684034
## 59: 0.005261677 -1.1191772 0.8688403 0.4684034
## 60: 0.005261677 -1.1191772 0.8688403 0.4684034
## 61: 0.005261677 -1.1191772 0.8688403 0.4684034
## 62: 0.005261677 -1.1191772 0.8688403 0.4684034
## 63: 0.005261677 -1.1191772 0.8688403 0.4684034
## 64: 0.005261677 -1.1191772 0.8688403 0.4684034
## 65: 0.005261677 -1.1191772 0.8688403 0.4684034
## 66: 0.005261677 -1.1191772 0.8688403 0.4684034
## 67: 0.005261677 -1.1191772 0.8688403 0.4684034
## 68: 0.005261677 -1.1191772 0.8688403 0.4684034
## 69: 0.005261677 -1.1191772 0.8688403 0.4684034
## 70: 0.005261677 -1.1191772 0.8688403 0.4684034
## 71: 0.005261677 -1.1191772 0.8688403 0.4684034
## 72: 0.005261677 -1.1191772 0.8688403 0.4684034
## 73: 0.005261677 -1.1191772 0.8688403 0.4684034
## 74: 0.005261677 -1.1191772 0.8688403 0.4684034
## 75: 0.005261677 -1.1191772 0.8688403 0.4684034
## 76: 0.005261677 -1.1191772 0.8688403 0.4684034
## 77: 0.005245917 -0.8139770 1.0031408 0.7004716
## 78: 0.004284669 -0.4169704 1.2196713 0.9030615
## 79: 0.004284669 -0.4169704 1.2196713 0.9030615
## se.bp v c pchi
## [1] "ORF32" "ORF9" "ORF67_1" "ORF59" "ORF36" "ORF8" "ORF39"## [1] 7## [1] "ORF2" "ORF3" "ORF11" "ORF14" "ORF18" "ORF19" "ORF26"
## [8] "ORF28" "ORF29" "ORF37" "ORF49" "ORF51" "ORF55" "ORF66_1"
## [15] "ORF73" "ORF74" "ORF76" "ORF64_1" "ORF75"## [1] 19Clustering statistics: Cluster number: 7
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 2: 1 ORF5 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 3: 1 ORF10 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 4: 1 ORF17 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 5: 1 ORF30 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 6: 1 ORF32 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 7: 1 ORF53 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 8: 1 ORF63 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 9: 1 ORF65_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 10: 1 ORF67_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 11: 1 ORF69 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 12: 1 NOIR_2 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 13: 2 ORF2 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 14: 2 ORF3 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 15: 2 ORF11 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 16: 2 ORF14 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 17: 2 ORF18 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 18: 2 ORF19 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 19: 2 ORF26 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 20: 2 ORF28 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 21: 2 ORF29 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 22: 2 ORF37 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 23: 2 ORF49 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 24: 2 ORF51 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 25: 2 ORF55 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 26: 2 ORF66_1 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 27: 2 ORF73 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 28: 2 ORF74 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 29: 2 ORF76 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 30: 3 ORF4 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 31: 3 ORF7 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 32: 3 ORF9 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 33: 3 ORF20 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 34: 3 ORF21 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 35: 3 ORF31 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 36: 3 ORF34 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 37: 3 ORF38 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 38: 3 ORF50 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 39: 3 ORF56 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 40: 3 ORF61 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 41: 3 NOIR_1 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 42: 4 ORF6 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 43: 4 ORF70 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 44: 5 ORF8 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 45: 5 ORF12 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 46: 5 ORF13 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 47: 5 ORF15 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 48: 5 ORF16 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 49: 5 ORF22 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 50: 5 ORF23 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 51: 5 ORF24 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 52: 5 ORF25 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 53: 5 ORF27 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 54: 5 ORF33 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 55: 5 ORF35.5 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 56: 5 ORF35 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 57: 5 ORF36 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 58: 5 ORF39 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 59: 5 CTO 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 60: 5 ORF40 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 61: 5 ORF41 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 62: 5 ORF42 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 63: 5 ORF43 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 64: 5 ORF44 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 65: 5 ORF46 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 66: 5 ORF48 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 67: 5 ORF52 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 68: 5 ORF54 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 69: 5 ORF57 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 70: 5 ORF58 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 71: 5 ORF59 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 72: 5 ORF60 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 73: 5 ORF62 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 74: 5 ORF68 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 75: 5 ORF71 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 76: 5 ORF72 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 77: 6 ORF45 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 78: 7 ORF64_1 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 79: 7 ORF75 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004412661 -1.9247386 1.0297672 0.6455362
## 2: 0.004412661 -1.9247386 1.0297672 0.6455362
## 3: 0.004412661 -1.9247386 1.0297672 0.6455362
## 4: 0.004412661 -1.9247386 1.0297672 0.6455362
## 5: 0.004412661 -1.9247386 1.0297672 0.6455362
## 6: 0.004412661 -1.9247386 1.0297672 0.6455362
## 7: 0.004412661 -1.9247386 1.0297672 0.6455362
## 8: 0.004412661 -1.9247386 1.0297672 0.6455362
## 9: 0.004412661 -1.9247386 1.0297672 0.6455362
## 10: 0.004412661 -1.9247386 1.0297672 0.6455362
## 11: 0.004412661 -1.9247386 1.0297672 0.6455362
## 12: 0.004412661 -1.9247386 1.0297672 0.6455362
## 13: 0.005151525 -0.8707344 0.5400240 0.2113619
## 14: 0.005151525 -0.8707344 0.5400240 0.2113619
## 15: 0.005151525 -0.8707344 0.5400240 0.2113619
## 16: 0.005151525 -0.8707344 0.5400240 0.2113619
## 17: 0.005151525 -0.8707344 0.5400240 0.2113619
## 18: 0.005151525 -0.8707344 0.5400240 0.2113619
## 19: 0.005151525 -0.8707344 0.5400240 0.2113619
## 20: 0.005151525 -0.8707344 0.5400240 0.2113619
## 21: 0.005151525 -0.8707344 0.5400240 0.2113619
## 22: 0.005151525 -0.8707344 0.5400240 0.2113619
## 23: 0.005151525 -0.8707344 0.5400240 0.2113619
## 24: 0.005151525 -0.8707344 0.5400240 0.2113619
## 25: 0.005151525 -0.8707344 0.5400240 0.2113619
## 26: 0.005151525 -0.8707344 0.5400240 0.2113619
## 27: 0.005151525 -0.8707344 0.5400240 0.2113619
## 28: 0.005151525 -0.8707344 0.5400240 0.2113619
## 29: 0.005151525 -0.8707344 0.5400240 0.2113619
## 30: 0.004425869 -1.9892346 1.0926661 0.5323203
## 31: 0.004425869 -1.9892346 1.0926661 0.5323203
## 32: 0.004425869 -1.9892346 1.0926661 0.5323203
## 33: 0.004425869 -1.9892346 1.0926661 0.5323203
## 34: 0.004425869 -1.9892346 1.0926661 0.5323203
## 35: 0.004425869 -1.9892346 1.0926661 0.5323203
## 36: 0.004425869 -1.9892346 1.0926661 0.5323203
## 37: 0.004425869 -1.9892346 1.0926661 0.5323203
## 38: 0.004425869 -1.9892346 1.0926661 0.5323203
## 39: 0.004425869 -1.9892346 1.0926661 0.5323203
## 40: 0.004425869 -1.9892346 1.0926661 0.5323203
## 41: 0.004425869 -1.9892346 1.0926661 0.5323203
## 42: 0.005261677 -1.1191772 0.8688403 0.4684034
## 43: 0.005261677 -1.1191772 0.8688403 0.4684034
## 44: 0.005245917 -0.8139770 1.0031408 0.7004716
## 45: 0.005245917 -0.8139770 1.0031408 0.7004716
## 46: 0.005245917 -0.8139770 1.0031408 0.7004716
## 47: 0.005245917 -0.8139770 1.0031408 0.7004716
## 48: 0.005245917 -0.8139770 1.0031408 0.7004716
## 49: 0.005245917 -0.8139770 1.0031408 0.7004716
## 50: 0.005245917 -0.8139770 1.0031408 0.7004716
## 51: 0.005245917 -0.8139770 1.0031408 0.7004716
## 52: 0.005245917 -0.8139770 1.0031408 0.7004716
## 53: 0.005245917 -0.8139770 1.0031408 0.7004716
## 54: 0.005245917 -0.8139770 1.0031408 0.7004716
## 55: 0.005245917 -0.8139770 1.0031408 0.7004716
## 56: 0.005245917 -0.8139770 1.0031408 0.7004716
## 57: 0.005245917 -0.8139770 1.0031408 0.7004716
## 58: 0.005245917 -0.8139770 1.0031408 0.7004716
## 59: 0.005245917 -0.8139770 1.0031408 0.7004716
## 60: 0.005245917 -0.8139770 1.0031408 0.7004716
## 61: 0.005245917 -0.8139770 1.0031408 0.7004716
## 62: 0.005245917 -0.8139770 1.0031408 0.7004716
## 63: 0.005245917 -0.8139770 1.0031408 0.7004716
## 64: 0.005245917 -0.8139770 1.0031408 0.7004716
## 65: 0.005245917 -0.8139770 1.0031408 0.7004716
## 66: 0.005245917 -0.8139770 1.0031408 0.7004716
## 67: 0.005245917 -0.8139770 1.0031408 0.7004716
## 68: 0.005245917 -0.8139770 1.0031408 0.7004716
## 69: 0.005245917 -0.8139770 1.0031408 0.7004716
## 70: 0.005245917 -0.8139770 1.0031408 0.7004716
## 71: 0.005245917 -0.8139770 1.0031408 0.7004716
## 72: 0.005245917 -0.8139770 1.0031408 0.7004716
## 73: 0.005245917 -0.8139770 1.0031408 0.7004716
## 74: 0.005245917 -0.8139770 1.0031408 0.7004716
## 75: 0.005245917 -0.8139770 1.0031408 0.7004716
## 76: 0.005245917 -0.8139770 1.0031408 0.7004716
## 77: 0.004284669 -0.4169704 1.2196713 0.9030615
## 78: 0.005111506 -0.7566956 1.0826127 0.7640431
## 79: 0.005111506 -0.7566956 1.0826127 0.7640431
## se.bp v c pchi
## [1] "ORF32" "ORF59" "ORF36" "ORF8" "ORF39"## [1] 5## [1] "ORF2" "ORF3" "ORF11" "ORF14" "ORF18" "ORF19" "ORF26"
## [8] "ORF28" "ORF29" "ORF37" "ORF49" "ORF51" "ORF55" "ORF66_1"
## [15] "ORF73" "ORF74" "ORF76" "ORF45"## [1] 18Clustering statistics: Cluster number: 10
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 2: 1 ORF5 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 3: 1 ORF10 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 4: 1 ORF17 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 5: 1 ORF30 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 6: 1 ORF53 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 7: 1 ORF63 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 8: 1 ORF65_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 9: 1 ORF67_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 10: 1 ORF69 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 11: 1 NOIR_2 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 12: 2 ORF2 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 13: 2 ORF3 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 14: 2 ORF11 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 15: 2 ORF14 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 16: 2 ORF18 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 17: 2 ORF19 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 18: 2 ORF26 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 19: 2 ORF29 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 20: 2 ORF37 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 21: 2 ORF49 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 22: 2 ORF51 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 23: 2 ORF55 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 24: 2 ORF66_1 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 25: 2 ORF73 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 26: 2 ORF74 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 27: 2 ORF76 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 28: 3 ORF4 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 29: 3 ORF7 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 30: 3 ORF9 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 31: 3 ORF20 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 32: 3 ORF21 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 33: 3 ORF31 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 34: 3 ORF34 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 35: 3 ORF38 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 36: 3 ORF50 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 37: 3 ORF56 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 38: 3 ORF61 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 39: 3 NOIR_1 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 40: 4 ORF6 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 41: 4 ORF70 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 42: 5 ORF8 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 43: 5 ORF22 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 44: 5 ORF23 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 45: 5 ORF24 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 46: 5 ORF25 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 47: 5 ORF27 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 48: 5 ORF33 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 49: 5 ORF35.5 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 50: 5 ORF36 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 51: 5 ORF39 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 52: 5 CTO 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 53: 5 ORF40 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 54: 5 ORF42 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 55: 5 ORF43 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 56: 5 ORF44 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 57: 5 ORF46 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 58: 5 ORF48 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 59: 5 ORF58 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 60: 5 ORF59 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 61: 5 ORF62 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 62: 5 ORF68 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 63: 6 ORF12 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 64: 6 ORF13 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 65: 6 ORF15 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 66: 6 ORF16 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 67: 6 ORF35 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 68: 6 ORF41 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 69: 6 ORF52 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 70: 6 ORF54 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 71: 6 ORF57 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 72: 6 ORF60 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 73: 6 ORF71 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 74: 6 ORF72 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 75: 7 ORF28 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 76: 8 ORF32 0.6869720 0.9523903 0.3495623 0.035110047 0.0082481844
## 77: 9 ORF45 0.8343762 0.9755240 0.4510585 0.021326740 0.0045952270
## 78: 10 ORF64_1 0.6967433 0.9667678 0.2669040 0.038592190 0.0067027536
## 79: 10 ORF75 0.6967433 0.9667678 0.2669040 0.038592190 0.0067027536
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004412661 -1.9247386 1.0297672 0.6455362
## 2: 0.004412661 -1.9247386 1.0297672 0.6455362
## 3: 0.004412661 -1.9247386 1.0297672 0.6455362
## 4: 0.004412661 -1.9247386 1.0297672 0.6455362
## 5: 0.004412661 -1.9247386 1.0297672 0.6455362
## 6: 0.004412661 -1.9247386 1.0297672 0.6455362
## 7: 0.004412661 -1.9247386 1.0297672 0.6455362
## 8: 0.004412661 -1.9247386 1.0297672 0.6455362
## 9: 0.004412661 -1.9247386 1.0297672 0.6455362
## 10: 0.004412661 -1.9247386 1.0297672 0.6455362
## 11: 0.004412661 -1.9247386 1.0297672 0.6455362
## 12: 0.005151525 -0.8707344 0.5400240 0.2113619
## 13: 0.005151525 -0.8707344 0.5400240 0.2113619
## 14: 0.005151525 -0.8707344 0.5400240 0.2113619
## 15: 0.005151525 -0.8707344 0.5400240 0.2113619
## 16: 0.005151525 -0.8707344 0.5400240 0.2113619
## 17: 0.005151525 -0.8707344 0.5400240 0.2113619
## 18: 0.005151525 -0.8707344 0.5400240 0.2113619
## 19: 0.005151525 -0.8707344 0.5400240 0.2113619
## 20: 0.005151525 -0.8707344 0.5400240 0.2113619
## 21: 0.005151525 -0.8707344 0.5400240 0.2113619
## 22: 0.005151525 -0.8707344 0.5400240 0.2113619
## 23: 0.005151525 -0.8707344 0.5400240 0.2113619
## 24: 0.005151525 -0.8707344 0.5400240 0.2113619
## 25: 0.005151525 -0.8707344 0.5400240 0.2113619
## 26: 0.005151525 -0.8707344 0.5400240 0.2113619
## 27: 0.005151525 -0.8707344 0.5400240 0.2113619
## 28: 0.004425869 -1.9892346 1.0926661 0.5323203
## 29: 0.004425869 -1.9892346 1.0926661 0.5323203
## 30: 0.004425869 -1.9892346 1.0926661 0.5323203
## 31: 0.004425869 -1.9892346 1.0926661 0.5323203
## 32: 0.004425869 -1.9892346 1.0926661 0.5323203
## 33: 0.004425869 -1.9892346 1.0926661 0.5323203
## 34: 0.004425869 -1.9892346 1.0926661 0.5323203
## 35: 0.004425869 -1.9892346 1.0926661 0.5323203
## 36: 0.004425869 -1.9892346 1.0926661 0.5323203
## 37: 0.004425869 -1.9892346 1.0926661 0.5323203
## 38: 0.004425869 -1.9892346 1.0926661 0.5323203
## 39: 0.004425869 -1.9892346 1.0926661 0.5323203
## 40: 0.005261677 -1.1191772 0.8688403 0.4684034
## 41: 0.005261677 -1.1191772 0.8688403 0.4684034
## 42: 0.005245917 -0.8139770 1.0031408 0.7004716
## 43: 0.005245917 -0.8139770 1.0031408 0.7004716
## 44: 0.005245917 -0.8139770 1.0031408 0.7004716
## 45: 0.005245917 -0.8139770 1.0031408 0.7004716
## 46: 0.005245917 -0.8139770 1.0031408 0.7004716
## 47: 0.005245917 -0.8139770 1.0031408 0.7004716
## 48: 0.005245917 -0.8139770 1.0031408 0.7004716
## 49: 0.005245917 -0.8139770 1.0031408 0.7004716
## 50: 0.005245917 -0.8139770 1.0031408 0.7004716
## 51: 0.005245917 -0.8139770 1.0031408 0.7004716
## 52: 0.005245917 -0.8139770 1.0031408 0.7004716
## 53: 0.005245917 -0.8139770 1.0031408 0.7004716
## 54: 0.005245917 -0.8139770 1.0031408 0.7004716
## 55: 0.005245917 -0.8139770 1.0031408 0.7004716
## 56: 0.005245917 -0.8139770 1.0031408 0.7004716
## 57: 0.005245917 -0.8139770 1.0031408 0.7004716
## 58: 0.005245917 -0.8139770 1.0031408 0.7004716
## 59: 0.005245917 -0.8139770 1.0031408 0.7004716
## 60: 0.005245917 -0.8139770 1.0031408 0.7004716
## 61: 0.005245917 -0.8139770 1.0031408 0.7004716
## 62: 0.005245917 -0.8139770 1.0031408 0.7004716
## 63: 0.004284669 -0.4169704 1.2196713 0.9030615
## 64: 0.004284669 -0.4169704 1.2196713 0.9030615
## 65: 0.004284669 -0.4169704 1.2196713 0.9030615
## 66: 0.004284669 -0.4169704 1.2196713 0.9030615
## 67: 0.004284669 -0.4169704 1.2196713 0.9030615
## 68: 0.004284669 -0.4169704 1.2196713 0.9030615
## 69: 0.004284669 -0.4169704 1.2196713 0.9030615
## 70: 0.004284669 -0.4169704 1.2196713 0.9030615
## 71: 0.004284669 -0.4169704 1.2196713 0.9030615
## 72: 0.004284669 -0.4169704 1.2196713 0.9030615
## 73: 0.004284669 -0.4169704 1.2196713 0.9030615
## 74: 0.004284669 -0.4169704 1.2196713 0.9030615
## 75: 0.005111506 -0.7566956 1.0826127 0.7640431
## 76: 0.005030398 -0.6409917 1.0274941 0.1121456
## 77: 0.005288863 -0.9230106 1.0459982 0.4260979
## 78: 0.004655777 -0.6065374 1.2287410 0.6115571
## 79: 0.004655777 -0.6065374 1.2287410 0.6115571
## se.bp v c pchi
## [1] "ORF49" "ORF74" "ORF55" "ORF73" "ORF62" "ORF48"## [1] 6## [1] "ORF2" "ORF3" "ORF11" "ORF14" "ORF18" "ORF19" "ORF26"
## [8] "ORF29" "ORF37" "ORF49" "ORF51" "ORF55" "ORF66_1" "ORF73"
## [15] "ORF74" "ORF76" "ORF12" "ORF13" "ORF15" "ORF16" "ORF35"
## [22] "ORF41" "ORF52" "ORF54" "ORF57" "ORF60" "ORF71" "ORF72"## [1] 28Clustering statistics: Cluster number: 12
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 2: 1 ORF5 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 3: 1 ORF10 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 4: 1 ORF17 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 5: 1 ORF30 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 6: 1 ORF53 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 7: 1 ORF63 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 8: 1 ORF65_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 9: 1 ORF67_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 10: 1 ORF69 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 11: 1 NOIR_2 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 12: 2 ORF2 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 13: 2 ORF3 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 14: 2 ORF11 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 15: 2 ORF14 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 16: 2 ORF18 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 17: 2 ORF19 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 18: 2 ORF26 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 19: 2 ORF29 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 20: 2 ORF49 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 21: 2 ORF66_1 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 22: 2 ORF73 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 23: 2 ORF74 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 24: 3 ORF4 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 25: 3 ORF9 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 26: 3 ORF20 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 27: 3 ORF21 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 28: 3 ORF31 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 29: 3 ORF34 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 30: 3 ORF38 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 31: 3 ORF50 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 32: 3 ORF61 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 33: 4 ORF6 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 34: 4 ORF70 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 35: 5 ORF7 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 36: 5 ORF56 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 37: 5 NOIR_1 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 38: 6 ORF8 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 39: 6 ORF22 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 40: 6 ORF23 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 41: 6 ORF24 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 42: 6 ORF25 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 43: 6 ORF27 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 44: 6 ORF33 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 45: 6 ORF35.5 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 46: 6 ORF36 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 47: 6 ORF39 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 48: 6 CTO 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 49: 6 ORF40 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 50: 6 ORF42 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 51: 6 ORF43 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 52: 6 ORF44 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 53: 6 ORF46 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 54: 6 ORF48 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 55: 6 ORF58 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 56: 6 ORF59 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 57: 6 ORF62 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 58: 6 ORF68 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 59: 7 ORF12 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 60: 7 ORF13 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 61: 7 ORF15 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 62: 7 ORF16 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 63: 7 ORF35 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 64: 7 ORF41 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 65: 7 ORF52 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 66: 7 ORF54 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 67: 7 ORF57 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 68: 7 ORF60 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 69: 7 ORF71 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 70: 7 ORF72 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 71: 8 ORF28 0.6869720 0.9523903 0.3495623 0.035110047 0.0082481844
## 72: 9 ORF32 0.8343762 0.9755240 0.4510585 0.021326740 0.0045952270
## 73: 10 ORF37 0.6967433 0.9667678 0.2669040 0.038592190 0.0067027536
## 74: 10 ORF51 0.6967433 0.9667678 0.2669040 0.038592190 0.0067027536
## 75: 10 ORF55 0.6967433 0.9667678 0.2669040 0.038592190 0.0067027536
## 76: 10 ORF76 0.6967433 0.9667678 0.2669040 0.038592190 0.0067027536
## 77: 11 ORF45 0.8717656 0.9745309 0.6021179 0.016716342 0.0046060056
## 78: 12 ORF64_1 0.6107119 0.9614072 0.2102031 0.048906177 0.0079641798
## 79: 12 ORF75 0.6107119 0.9614072 0.2102031 0.048906177 0.0079641798
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004412661 -1.9247386 1.0297672 0.6455362
## 2: 0.004412661 -1.9247386 1.0297672 0.6455362
## 3: 0.004412661 -1.9247386 1.0297672 0.6455362
## 4: 0.004412661 -1.9247386 1.0297672 0.6455362
## 5: 0.004412661 -1.9247386 1.0297672 0.6455362
## 6: 0.004412661 -1.9247386 1.0297672 0.6455362
## 7: 0.004412661 -1.9247386 1.0297672 0.6455362
## 8: 0.004412661 -1.9247386 1.0297672 0.6455362
## 9: 0.004412661 -1.9247386 1.0297672 0.6455362
## 10: 0.004412661 -1.9247386 1.0297672 0.6455362
## 11: 0.004412661 -1.9247386 1.0297672 0.6455362
## 12: 0.005151525 -0.8707344 0.5400240 0.2113619
## 13: 0.005151525 -0.8707344 0.5400240 0.2113619
## 14: 0.005151525 -0.8707344 0.5400240 0.2113619
## 15: 0.005151525 -0.8707344 0.5400240 0.2113619
## 16: 0.005151525 -0.8707344 0.5400240 0.2113619
## 17: 0.005151525 -0.8707344 0.5400240 0.2113619
## 18: 0.005151525 -0.8707344 0.5400240 0.2113619
## 19: 0.005151525 -0.8707344 0.5400240 0.2113619
## 20: 0.005151525 -0.8707344 0.5400240 0.2113619
## 21: 0.005151525 -0.8707344 0.5400240 0.2113619
## 22: 0.005151525 -0.8707344 0.5400240 0.2113619
## 23: 0.005151525 -0.8707344 0.5400240 0.2113619
## 24: 0.004425869 -1.9892346 1.0926661 0.5323203
## 25: 0.004425869 -1.9892346 1.0926661 0.5323203
## 26: 0.004425869 -1.9892346 1.0926661 0.5323203
## 27: 0.004425869 -1.9892346 1.0926661 0.5323203
## 28: 0.004425869 -1.9892346 1.0926661 0.5323203
## 29: 0.004425869 -1.9892346 1.0926661 0.5323203
## 30: 0.004425869 -1.9892346 1.0926661 0.5323203
## 31: 0.004425869 -1.9892346 1.0926661 0.5323203
## 32: 0.004425869 -1.9892346 1.0926661 0.5323203
## 33: 0.005261677 -1.1191772 0.8688403 0.4684034
## 34: 0.005261677 -1.1191772 0.8688403 0.4684034
## 35: 0.005245917 -0.8139770 1.0031408 0.7004716
## 36: 0.005245917 -0.8139770 1.0031408 0.7004716
## 37: 0.005245917 -0.8139770 1.0031408 0.7004716
## 38: 0.004284669 -0.4169704 1.2196713 0.9030615
## 39: 0.004284669 -0.4169704 1.2196713 0.9030615
## 40: 0.004284669 -0.4169704 1.2196713 0.9030615
## 41: 0.004284669 -0.4169704 1.2196713 0.9030615
## 42: 0.004284669 -0.4169704 1.2196713 0.9030615
## 43: 0.004284669 -0.4169704 1.2196713 0.9030615
## 44: 0.004284669 -0.4169704 1.2196713 0.9030615
## 45: 0.004284669 -0.4169704 1.2196713 0.9030615
## 46: 0.004284669 -0.4169704 1.2196713 0.9030615
## 47: 0.004284669 -0.4169704 1.2196713 0.9030615
## 48: 0.004284669 -0.4169704 1.2196713 0.9030615
## 49: 0.004284669 -0.4169704 1.2196713 0.9030615
## 50: 0.004284669 -0.4169704 1.2196713 0.9030615
## 51: 0.004284669 -0.4169704 1.2196713 0.9030615
## 52: 0.004284669 -0.4169704 1.2196713 0.9030615
## 53: 0.004284669 -0.4169704 1.2196713 0.9030615
## 54: 0.004284669 -0.4169704 1.2196713 0.9030615
## 55: 0.004284669 -0.4169704 1.2196713 0.9030615
## 56: 0.004284669 -0.4169704 1.2196713 0.9030615
## 57: 0.004284669 -0.4169704 1.2196713 0.9030615
## 58: 0.004284669 -0.4169704 1.2196713 0.9030615
## 59: 0.005111506 -0.7566956 1.0826127 0.7640431
## 60: 0.005111506 -0.7566956 1.0826127 0.7640431
## 61: 0.005111506 -0.7566956 1.0826127 0.7640431
## 62: 0.005111506 -0.7566956 1.0826127 0.7640431
## 63: 0.005111506 -0.7566956 1.0826127 0.7640431
## 64: 0.005111506 -0.7566956 1.0826127 0.7640431
## 65: 0.005111506 -0.7566956 1.0826127 0.7640431
## 66: 0.005111506 -0.7566956 1.0826127 0.7640431
## 67: 0.005111506 -0.7566956 1.0826127 0.7640431
## 68: 0.005111506 -0.7566956 1.0826127 0.7640431
## 69: 0.005111506 -0.7566956 1.0826127 0.7640431
## 70: 0.005111506 -0.7566956 1.0826127 0.7640431
## 71: 0.005030398 -0.6409917 1.0274941 0.1121456
## 72: 0.005288863 -0.9230106 1.0459982 0.4260979
## 73: 0.004655777 -0.6065374 1.2287410 0.6115571
## 74: 0.004655777 -0.6065374 1.2287410 0.6115571
## 75: 0.004655777 -0.6065374 1.2287410 0.6115571
## 76: 0.004655777 -0.6065374 1.2287410 0.6115571
## 77: 0.005269934 -1.1054164 0.8465835 0.5423247
## 78: 0.004283939 -0.4807691 1.2864858 0.2612100
## 79: 0.004283939 -0.4807691 1.2864858 0.2612100
## se.bp v c pchi
## [1] "NOIR_2" "ORF1" "ORF36" "ORF59" "ORF8" "ORF39" "ORF62" "ORF48"## [1] 8## [1] "ORF2" "ORF3" "ORF11" "ORF14" "ORF18" "ORF19" "ORF26"
## [8] "ORF29" "ORF49" "ORF66_1" "ORF73" "ORF74" "ORF8" "ORF22"
## [15] "ORF23" "ORF24" "ORF25" "ORF27" "ORF33" "ORF35.5" "ORF36"
## [22] "ORF39" "CTO" "ORF40" "ORF42" "ORF43" "ORF44" "ORF46"
## [29] "ORF48" "ORF58" "ORF59" "ORF62" "ORF68"## [1] 33Selected number of clusters: 12
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 2: 1 ORF5 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 3: 1 ORF10 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 4: 1 ORF17 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 5: 1 ORF30 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 6: 1 ORF53 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 7: 1 ORF63 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 8: 1 ORF65_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 9: 1 ORF67_1 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 10: 1 ORF69 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 11: 1 NOIR_2 0.9896684 0.9984341 0.8145988 0.002282700 0.0004400972
## 12: 2 ORF2 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 13: 2 ORF3 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 14: 2 ORF11 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 15: 2 ORF14 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 16: 2 ORF18 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 17: 2 ORF19 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 18: 2 ORF26 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 19: 2 ORF29 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 20: 2 ORF49 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 21: 2 ORF66_1 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 22: 2 ORF73 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 23: 2 ORF74 0.7312948 0.9208421 0.6295684 0.027238159 0.0113147725
## 24: 3 ORF4 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 25: 3 ORF9 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 26: 3 ORF20 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 27: 3 ORF21 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 28: 3 ORF31 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 29: 3 ORF34 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 30: 3 ORF38 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 31: 3 ORF50 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 32: 3 ORF61 0.9925081 0.9989716 0.8150254 0.001727305 0.0003012729
## 33: 4 ORF6 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 34: 4 ORF70 0.8783955 0.9765951 0.5988366 0.016082099 0.0042956202
## 35: 5 ORF7 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 36: 5 ORF56 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 37: 5 NOIR_1 0.7808720 0.9654005 0.4249822 0.026086231 0.0061073598
## 38: 6 ORF8 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 39: 6 ORF22 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 40: 6 ORF23 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 41: 6 ORF24 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 42: 6 ORF25 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 43: 6 ORF27 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 44: 6 ORF33 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 45: 6 ORF35.5 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 46: 6 ORF36 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 47: 6 ORF39 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 48: 6 CTO 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 49: 6 ORF40 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 50: 6 ORF42 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 51: 6 ORF43 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 52: 6 ORF44 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 53: 6 ORF46 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 54: 6 ORF48 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 55: 6 ORF58 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 56: 6 ORF59 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 57: 6 ORF62 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 58: 6 ORF68 0.5430810 0.9491473 0.2110738 0.053336441 0.0098715132
## 59: 7 ORF12 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 60: 7 ORF13 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 61: 7 ORF15 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 62: 7 ORF16 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 63: 7 ORF35 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 64: 7 ORF41 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 65: 7 ORF52 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 66: 7 ORF54 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 67: 7 ORF57 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 68: 7 ORF60 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 69: 7 ORF71 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 70: 7 ORF72 0.7638907 0.9670651 0.3722436 0.028677226 0.0060467326
## 71: 8 ORF28 0.6869720 0.9523903 0.3495623 0.035110047 0.0082481844
## 72: 9 ORF32 0.8343762 0.9755240 0.4510585 0.021326740 0.0045952270
## 73: 10 ORF37 0.6967433 0.9667678 0.2669040 0.038592190 0.0067027536
## 74: 10 ORF51 0.6967433 0.9667678 0.2669040 0.038592190 0.0067027536
## 75: 10 ORF55 0.6967433 0.9667678 0.2669040 0.038592190 0.0067027536
## 76: 10 ORF76 0.6967433 0.9667678 0.2669040 0.038592190 0.0067027536
## 77: 11 ORF45 0.8717656 0.9745309 0.6021179 0.016716342 0.0046060056
## 78: 12 ORF64_1 0.6107119 0.9614072 0.2102031 0.048906177 0.0079641798
## 79: 12 ORF75 0.6107119 0.9614072 0.2102031 0.048906177 0.0079641798
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004412661 -1.9247386 1.0297672 0.6455362
## 2: 0.004412661 -1.9247386 1.0297672 0.6455362
## 3: 0.004412661 -1.9247386 1.0297672 0.6455362
## 4: 0.004412661 -1.9247386 1.0297672 0.6455362
## 5: 0.004412661 -1.9247386 1.0297672 0.6455362
## 6: 0.004412661 -1.9247386 1.0297672 0.6455362
## 7: 0.004412661 -1.9247386 1.0297672 0.6455362
## 8: 0.004412661 -1.9247386 1.0297672 0.6455362
## 9: 0.004412661 -1.9247386 1.0297672 0.6455362
## 10: 0.004412661 -1.9247386 1.0297672 0.6455362
## 11: 0.004412661 -1.9247386 1.0297672 0.6455362
## 12: 0.005151525 -0.8707344 0.5400240 0.2113619
## 13: 0.005151525 -0.8707344 0.5400240 0.2113619
## 14: 0.005151525 -0.8707344 0.5400240 0.2113619
## 15: 0.005151525 -0.8707344 0.5400240 0.2113619
## 16: 0.005151525 -0.8707344 0.5400240 0.2113619
## 17: 0.005151525 -0.8707344 0.5400240 0.2113619
## 18: 0.005151525 -0.8707344 0.5400240 0.2113619
## 19: 0.005151525 -0.8707344 0.5400240 0.2113619
## 20: 0.005151525 -0.8707344 0.5400240 0.2113619
## 21: 0.005151525 -0.8707344 0.5400240 0.2113619
## 22: 0.005151525 -0.8707344 0.5400240 0.2113619
## 23: 0.005151525 -0.8707344 0.5400240 0.2113619
## 24: 0.004425869 -1.9892346 1.0926661 0.5323203
## 25: 0.004425869 -1.9892346 1.0926661 0.5323203
## 26: 0.004425869 -1.9892346 1.0926661 0.5323203
## 27: 0.004425869 -1.9892346 1.0926661 0.5323203
## 28: 0.004425869 -1.9892346 1.0926661 0.5323203
## 29: 0.004425869 -1.9892346 1.0926661 0.5323203
## 30: 0.004425869 -1.9892346 1.0926661 0.5323203
## 31: 0.004425869 -1.9892346 1.0926661 0.5323203
## 32: 0.004425869 -1.9892346 1.0926661 0.5323203
## 33: 0.005261677 -1.1191772 0.8688403 0.4684034
## 34: 0.005261677 -1.1191772 0.8688403 0.4684034
## 35: 0.005245917 -0.8139770 1.0031408 0.7004716
## 36: 0.005245917 -0.8139770 1.0031408 0.7004716
## 37: 0.005245917 -0.8139770 1.0031408 0.7004716
## 38: 0.004284669 -0.4169704 1.2196713 0.9030615
## 39: 0.004284669 -0.4169704 1.2196713 0.9030615
## 40: 0.004284669 -0.4169704 1.2196713 0.9030615
## 41: 0.004284669 -0.4169704 1.2196713 0.9030615
## 42: 0.004284669 -0.4169704 1.2196713 0.9030615
## 43: 0.004284669 -0.4169704 1.2196713 0.9030615
## 44: 0.004284669 -0.4169704 1.2196713 0.9030615
## 45: 0.004284669 -0.4169704 1.2196713 0.9030615
## 46: 0.004284669 -0.4169704 1.2196713 0.9030615
## 47: 0.004284669 -0.4169704 1.2196713 0.9030615
## 48: 0.004284669 -0.4169704 1.2196713 0.9030615
## 49: 0.004284669 -0.4169704 1.2196713 0.9030615
## 50: 0.004284669 -0.4169704 1.2196713 0.9030615
## 51: 0.004284669 -0.4169704 1.2196713 0.9030615
## 52: 0.004284669 -0.4169704 1.2196713 0.9030615
## 53: 0.004284669 -0.4169704 1.2196713 0.9030615
## 54: 0.004284669 -0.4169704 1.2196713 0.9030615
## 55: 0.004284669 -0.4169704 1.2196713 0.9030615
## 56: 0.004284669 -0.4169704 1.2196713 0.9030615
## 57: 0.004284669 -0.4169704 1.2196713 0.9030615
## 58: 0.004284669 -0.4169704 1.2196713 0.9030615
## 59: 0.005111506 -0.7566956 1.0826127 0.7640431
## 60: 0.005111506 -0.7566956 1.0826127 0.7640431
## 61: 0.005111506 -0.7566956 1.0826127 0.7640431
## 62: 0.005111506 -0.7566956 1.0826127 0.7640431
## 63: 0.005111506 -0.7566956 1.0826127 0.7640431
## 64: 0.005111506 -0.7566956 1.0826127 0.7640431
## 65: 0.005111506 -0.7566956 1.0826127 0.7640431
## 66: 0.005111506 -0.7566956 1.0826127 0.7640431
## 67: 0.005111506 -0.7566956 1.0826127 0.7640431
## 68: 0.005111506 -0.7566956 1.0826127 0.7640431
## 69: 0.005111506 -0.7566956 1.0826127 0.7640431
## 70: 0.005111506 -0.7566956 1.0826127 0.7640431
## 71: 0.005030398 -0.6409917 1.0274941 0.1121456
## 72: 0.005288863 -0.9230106 1.0459982 0.4260979
## 73: 0.004655777 -0.6065374 1.2287410 0.6115571
## 74: 0.004655777 -0.6065374 1.2287410 0.6115571
## 75: 0.004655777 -0.6065374 1.2287410 0.6115571
## 76: 0.004655777 -0.6065374 1.2287410 0.6115571
## 77: 0.005269934 -1.1054164 0.8465835 0.5423247
## 78: 0.004283939 -0.4807691 1.2864858 0.2612100
## 79: 0.004283939 -0.4807691 1.2864858 0.2612100
## se.bp v c pchi
## [1] "NOIR_2" "ORF1" "ORF36" "ORF59" "ORF8" "ORF39" "ORF62" "ORF48"## [1] 8## [1] "ORF2" "ORF3" "ORF11" "ORF14" "ORF18" "ORF19" "ORF26"
## [8] "ORF29" "ORF49" "ORF66_1" "ORF73" "ORF74" "ORF8" "ORF22"
## [15] "ORF23" "ORF24" "ORF25" "ORF27" "ORF33" "ORF35.5" "ORF36"
## [22] "ORF39" "CTO" "ORF40" "ORF42" "ORF43" "ORF44" "ORF46"
## [29] "ORF48" "ORF58" "ORF59" "ORF62" "ORF68"## [1] 33Remove genes from clusters ?
## [1] "ORF2" "ORF3" "ORF11" "ORF14" "ORF18" "ORF19" "ORF26"
## [8] "ORF29" "ORF49" "ORF66_1" "ORF73" "ORF74" "ORF8" "ORF22"
## [15] "ORF23" "ORF24" "ORF25" "ORF27" "ORF33" "ORF35.5" "ORF36"
## [22] "ORF39" "CTO" "ORF40" "ORF42" "ORF43" "ORF44" "ORF46"
## [29] "ORF48" "ORF58" "ORF59" "ORF62" "ORF68"## [1] 33## No genes were removed from their corresponding clusters.## cluster N
## <int> <int>
## 1: 6 21
## 2: 2 12
## 3: 7 12
## 4: 1 11
## 5: 3 9
## 6: 10 4
## 7: 5 3
## 8: 4 2
## 9: 12 2
## 10: 8 1
## 11: 9 1
## 12: 11 1Merge cluster stats
Assigning genes to clusters
Summarize and melt
Heatmaps
Normalized Expression
Expression delta ~ 6 hpi
Z-score of expression delta ~ 6 hpi
ORF kinetics, according to literature-based kinetic classes
Barplot of mean and SD
Figure 4 REVIEW - Mean and SD with linear connection
Mean and SD with loess function
Mean and SD with linear connection - Figure 4
Each replicate with loess
ORF kinetics, according to de-novo kinetic classes
Mean and SD with linear connection
Figure 5 REVIEW - Mean and SD with linear connection
Compare literature and de novo kinetic classes
NA shows the number of genes where the clustering did not yield an unambiguous result.
Combined Kinetic classes
De Novo Clusters
Literature clusters
